We have an MS and a new Model 3. If you are chosing between the two models I think the first question is how large of a car do you need. The Model S just has a wonderful amount of cargo area (about twice that of the Model 3 in cubic feet), and that space is configured differently. Lift gates do provide you with space (in height) that you won't get in the Model 3.
Along the lines of space, if you will be having passengers regularly in the second row, I think the Model S is the more comfortable car for them. The Model 3 is a great car and still spacious, but I think the Model S is a more luxurious car for adults if they will be using both rows. I'd say the Model 3 is a sportier car to drive while not being a convertible if that feel is more important to you. If parking is an issue where you live, the Model 3 will be easier to park being a little bit smaller.
Depending on the battery configuration, you'll need to weigh which gives you more range if you think that will be a factor for you. Regular daily trips weighed against longer trips if you travel. Having more range is a nice convenience feature whether it's in frequency of needing to charge especially if you can't charge at home or in allowing you to travel further between Superchargers on a trip for example. Keep in mind most people will keep their battery between 20-80% charged. If you live in a cold (heater) or hot (AC) climate that will affect your battery range as well.
Autopilot's features, especially TACC with setting the car spacing and adjusting to the speed of the car in front of you, is nice to have. We don't happen to use our autosteer but many love it for highway driving. The Model 3 will have a newer screen, albeit it is smaller but very sharp. I personally love the the Model S large 17-inch screen. The processor speed in the Model 3 will be faster I believe. Our 3/2017 Model S has AM and FM radio, which might be important to some. The AM reception is spotty depending on where you are.
As for comfort, the seats will be different. Different bolstering, different materials. You'll find threads with differing viewpoints on comfort on both. Our Model S has the perforated leather and our seat ventilation works very well in our car. We have taken a few trips during the hot, dry California summers with black interior these past 2 years and never really felt our backs or legs on the seats perspired or felt overheated. Haven't had a chance to do any similar trips in our Model 3 but don't think the seats will "breathe" like our Model S seats. The ventilated seating was not widely available on the Model S so may not be a factor but did want to mention it. Based on our Model S experience we would have ordered it for our Model 3 if it had been available.
I love having a pano roof and being able to open it. Would have ordered one on our Model 3 if it had been available. However, it's not something everyone wants.